[1] His parents were William the Rich, Duke of Jülich-Cleves-Berg (1516–1592) and Maria of Austria (1531–1581), a daughter of Ferdinand I, Holy Roman Emperor and Anna of Bohemia and Hungary.

However, after the unexpected death of his elder brother Karl Friedrich, Wilhelm was needed to succeed his father as Duke of Jülich-Cleves-Berg, a secular fief.

[2][3] However, no substantial evidence of a relation between Anna and Johann Wilhelm, Duke of Jülich-Cleves-Berg has ever been presented.

Johann Wilhelm was subject to a serious mental illness,[4] for which he was treated by the physician Francesco Maria Guazzo.

[4] Upon Johann Wilhelm's death in 1609, his inheritance was claimed by the heirs of his two eldest sisters: the heir of Maria Eleonora of Cleves (1550–1608), the eldest sister and married to Albert Frederick, Duke of Prussia, was Anna of Prussia, the Electress of Brandenburg, a Protestant.